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Doc: Lassen Stays TOSS3, Fix SciPy (#5063)
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Sadly, the TOSS4 transition was not completed before the IBM contract ran out and Lassen stays with TOSS3. This simplifies the documentation again.
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@ax3l
ax3l authored Jul 19, 2024
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161 changes: 31 additions & 130 deletions Docs/source/install/hpc/lassen.rst
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Expand Up @@ -24,27 +24,9 @@ If you are new to this system, **please see the following resources**:
Login
-----

.. tab-set::

.. tab-item:: TOSS4 (RHEL8)

Lassen is currently transitioning to RHEL8.
During this transition, first SSH into lassen and then to the updated RHEL8/TOSS4 nodes.

.. code-block:: bash
ssh lassen.llnl.gov
ssh eatoss4
Approximately October/November 2023, the new software environment on these nodes will be the new default.

.. tab-item:: TOSS3 (RHEL7)

.. code-block:: bash
ssh lassen.llnl.gov
.. code-block:: bash
Approximately October/November 2023, this partition will become TOSS4 (RHEL8) as well.
ssh lassen.llnl.gov
.. _building-lassen-preparation:
Expand All @@ -58,135 +40,54 @@ Use the following commands to download the WarpX source code:
git clone https://github.com/ECP-WarpX/WarpX.git /usr/workspace/${USER}/lassen/src/warpx
.. tab-set::

.. tab-item:: TOSS4 (RHEL8)

We use system software modules, add environment hints and further dependencies via the file ``$HOME/lassen_v100_warpx.profile``.
Create it now:

.. code-block:: bash
cp /usr/workspace/${USER}/lassen/src/warpx/Tools/machines/lassen-llnl/lassen_v100_warpx.profile.example $HOME/lassen_v100_warpx.profile
.. dropdown:: Script Details
:color: light
:icon: info
:animate: fade-in-slide-down

.. literalinclude:: ../../../../Tools/machines/lassen-llnl/lassen_v100_warpx.profile.example
:language: bash

Edit the 2nd line of this script, which sets the ``export proj=""`` variable.
For example, if you are member of the project ``nsldt``, then run ``vi $HOME/lassen_v100_warpx.profile``.
Enter the edit mode by typing ``i`` and edit line 2 to read:

.. code-block:: bash
export proj="nsldt"
Exit the ``vi`` editor with ``Esc`` and then type ``:wq`` (write & quit).

.. important::

Now, and as the first step on future logins to lassen, activate these environment settings:

.. code-block:: bash
We use system software modules, add environment hints and further dependencies via the file ``$HOME/lassen_v100_warpx_toss3.profile``.
Create it now:

source $HOME/lassen_v100_warpx.profile
.. tab-item:: TOSS3 (RHEL7)

We use system software modules, add environment hints and further dependencies via the file ``$HOME/lassen_v100_warpx_toss3.profile``.
Create it now:

.. code-block:: bash
.. code-block:: bash
cp /usr/workspace/${USER}/lassen/src/warpx/Tools/machines/lassen-llnl/lassen_v100_warpx_toss3.profile.example $HOME/lassen_v100_warpx_toss3.profile
cp /usr/workspace/${USER}/lassen/src/warpx/Tools/machines/lassen-llnl/lassen_v100_warpx_toss3.profile.example $HOME/lassen_v100_warpx_toss3.profile
.. dropdown:: Script Details
:color: light
:icon: info
:animate: fade-in-slide-down
.. dropdown:: Script Details
:color: light
:icon: info
:animate: fade-in-slide-down

.. literalinclude:: ../../../../Tools/machines/lassen-llnl/lassen_v100_warpx_toss3.profile.example
:language: bash
.. literalinclude:: ../../../../Tools/machines/lassen-llnl/lassen_v100_warpx_toss3.profile.example
:language: bash

Edit the 2nd line of this script, which sets the ``export proj=""`` variable.
For example, if you are member of the project ``nsldt``, then run ``vi $HOME/lassen_v100_warpx_toss3.profile``.
Enter the edit mode by typing ``i`` and edit line 2 to read:
Edit the 2nd line of this script, which sets the ``export proj=""`` variable.
For example, if you are member of the project ``nsldt``, then run ``vi $HOME/lassen_v100_warpx_toss3.profile``.
Enter the edit mode by typing ``i`` and edit line 2 to read:

.. code-block:: bash
.. code-block:: bash
export proj="nsldt"
export proj="nsldt"
Exit the ``vi`` editor with ``Esc`` and then type ``:wq`` (write & quit).
Exit the ``vi`` editor with ``Esc`` and then type ``:wq`` (write & quit).

.. important::
.. important::

Now, and as the first step on future logins to lassen, activate these environment settings:
Now, and as the first step on future logins to lassen, activate these environment settings:

.. code-block:: bash
.. code-block:: bash
source $HOME/lassen_v100_warpx_toss3.profile
source $HOME/lassen_v100_warpx_toss3.profile
Finally, since lassen does not yet provide software modules for some of our dependencies, install them once:

.. tab-set::

.. tab-item:: TOSS4 (RHEL8)

.. code-block:: bash
bash /usr/workspace/${USER}/lassen/src/warpx/Tools/machines/lassen-llnl/install_v100_dependencies.sh
source /usr/workspace/${USER}/lassen/gpu/venvs/warpx-lassen/bin/activate
.. dropdown:: Script Details
:color: light
:icon: info
:animate: fade-in-slide-down

.. literalinclude:: ../../../../Tools/machines/lassen-llnl/install_v100_dependencies.sh
:language: bash

.. dropdown:: AI/ML Dependencies (Optional)
:animate: fade-in-slide-down

If you plan to run AI/ML workflows depending on pyTorch, run the next step as well.
This will take a while and should be skipped if not needed.

.. code-block:: bash
runNode bash /usr/workspace/${USER}/lassen/src/warpx/Tools/machines/lassen-llnl/install_v100_ml.sh
.. dropdown:: Script Details
:color: light
:icon: info
:animate: fade-in-slide-down

.. literalinclude:: ../../../../Tools/machines/lassen-llnl/install_v100_ml.sh
:language: bash

For `optimas dependencies <https://github.com/optimas-org/optimas>`__ (incl. scikit-learn), plan another hour of build time:

.. code-block:: bash
python3 -m pip install -r /usr/workspace/${USER}/lassen/src/warpx/Tools/optimas/requirements.txt
.. tab-item:: TOSS3 (RHEL7)
.. code-block:: bash
.. code-block:: bash
bash /usr/workspace/${USER}/lassen/src/warpx/Tools/machines/lassen-llnl/install_v100_dependencies_toss3.sh
source /usr/workspace/${USER}/lassen-toss3/gpu/venvs/warpx-lassen-toss3/bin/activate
bash /usr/workspace/${USER}/lassen/src/warpx/Tools/machines/lassen-llnl/install_v100_dependencies_toss3.sh
source /usr/workspace/${USER}/lassen-toss3/gpu/venvs/warpx-lassen-toss3/bin/activate
.. dropdown:: Script Details
:color: light
:icon: info
:animate: fade-in-slide-down

.. dropdown:: Script Details
:color: light
:icon: info
:animate: fade-in-slide-down
.. literalinclude:: ../../../../Tools/machines/lassen-llnl/install_v100_dependencies_toss3.sh
:language: bash

.. literalinclude:: ../../../../Tools/machines/lassen-llnl/install_v100_dependencies_toss3.sh
:language: bash

.. _building-lassen-compilation:

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142 changes: 0 additions & 142 deletions Tools/machines/lassen-llnl/install_v100_dependencies.sh
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4 changes: 1 addition & 3 deletions Tools/machines/lassen-llnl/install_v100_dependencies_toss3.sh
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Expand Up @@ -119,9 +119,7 @@ python3 -m pip install --upgrade build
python3 -m pip install --upgrade packaging
python3 -m pip install --upgrade wheel
python3 -m pip install --upgrade setuptools
# Older version for h5py
# https://github.com/h5py/h5py/issues/2268
python3 -m pip install --upgrade "cython<3"
python3 -m pip install --upgrade cython
python3 -m pip install --upgrade numpy
python3 -m pip install --upgrade pandas
CMAKE_PREFIX_PATH=/usr/lib64:${CMAKE_PREFIX_PATH} python3 -m pip install --upgrade -Ccompile-args="-j10" -Csetup-args=-Dblas=BLAS -Csetup-args=-Dlapack=BLAS scipy
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